The study aimed to estimate the prevalence of smoking and alcohol intake among university students from the Federal University of Pelotas, Brazil (UFPel), as well as to investigate factors associated with both habits. The sample included 485 students who were admitted to the university in 2008. Students were sampled randomly across all schools of the UFPel campus, and answered a pre-tested questionnaire, which was administered in the classroom by a member of the research team. Of the individuals interviewed, 53.9% were females and 42.3% were under 20 years. Regarding alcohol intake, 75% used alcohol once a month or less frequently, and the prevalence of risk for abusive alcohol intake was 6.2%. Regarding smoking, 10.2% reported smoking regularly or on weekends. More than 90% of those who smoked or used alcohol started before entering the university. Smoking was directly related to age and inversely related to self-rated health. In terms of alcohol intake, those who lived with friends were more likely to use it. Our data suggest the need for implementing strategies to promote healthy lifestyles among university students. However, the fact that more than 90% of individuals started to smoke or drink before entering the university suggests that interventions should target adolescents as a whole, and not only those who are university students, because onset of smoking and alcohol intake seems to occur at earlier ages.